Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Point and Frameshift Mutations01:30

Point and Frameshift Mutations

46
Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
46
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

15.4K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
15.4K
Leaky Scanning02:28

Leaky Scanning

5.2K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.2K
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

5.9K
DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
5.9K
Viral Mutations00:36

Viral Mutations

32.7K
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
32.7K
Viruses with RNA Genomes01:29

Viruses with RNA Genomes

68
RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
68

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Single-cell map of the healthy human immune system across the lifespan reveals unique infant immune signatures.

Nature communications·2026
Same author

The Alberta Quality Assessment Tool: Risk of Bias (AQAT:RoB) for the Evaluation of Medical Large Language Model Question-Answer Studies: Development and Pilot Validation.

Journal of medical Internet research·2026
Same author

Neonicotinoid-induced signature dysbiosis identified via metagenomic sequencing of the honey bee gut microbiome.

Scientific reports·2025
Same author

Are the tools fit for purpose? Network inference algorithms evaluated on a simulated lipidomics network.

Bioinformatics advances·2025
Same author

Omics Insights Into the Effects of Highbush Blueberry and Cranberry Crop Agroecosystems on Honey Bee Health and Physiology.

Proteomics·2025
Same author

Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.

RNA (New York, N.Y.)·2025

Related Experiment Video

Updated: Aug 8, 2025

Production of Pseudotyped Particles to Study Highly Pathogenic Coronaviruses in a Biosafety Level 2 Setting
08:40

Production of Pseudotyped Particles to Study Highly Pathogenic Coronaviruses in a Biosafety Level 2 Setting

Published on: March 1, 2019

59.1K

Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot.

Luke Trinity1, Ian Wark2, Lance Lansing1

  • 1Department of Computer Science, University of Victoria, Victoria, British Columbia, Canada.

Plos Computational Biology
|February 28, 2023
PubMed
Summary
This summary is machine-generated.

Coronaviruses like SARS-CoV-2 use -1 programmed ribosomal frameshifting (-1 PRF) for replication. Understanding the SARS-CoV-2 -1 PRF pseudoknot structure is key to developing new therapies against COVID-19.

More Related Videos

Production of a SARS-CoV-2 Virus-Like-Particle System to Investigate Viral Life Cycles In Vitro
09:26

Production of a SARS-CoV-2 Virus-Like-Particle System to Investigate Viral Life Cycles In Vitro

Published on: June 6, 2025

478
Author Spotlight: Studying Host-Virus Interactions with Pseudotyped Viruses
05:49

Author Spotlight: Studying Host-Virus Interactions with Pseudotyped Viruses

Published on: November 21, 2023

1.8K

Related Experiment Videos

Last Updated: Aug 8, 2025

Production of Pseudotyped Particles to Study Highly Pathogenic Coronaviruses in a Biosafety Level 2 Setting
08:40

Production of Pseudotyped Particles to Study Highly Pathogenic Coronaviruses in a Biosafety Level 2 Setting

Published on: March 1, 2019

59.1K
Production of a SARS-CoV-2 Virus-Like-Particle System to Investigate Viral Life Cycles In Vitro
09:26

Production of a SARS-CoV-2 Virus-Like-Particle System to Investigate Viral Life Cycles In Vitro

Published on: June 6, 2025

478
Author Spotlight: Studying Host-Virus Interactions with Pseudotyped Viruses
05:49

Author Spotlight: Studying Host-Virus Interactions with Pseudotyped Viruses

Published on: November 21, 2023

1.8K

Area of Science:

  • Virology
  • Computational Biology
  • Structural Biology

Background:

  • Multiple coronaviruses, including SARS-CoV-2, SARS-CoV, and MERS-CoV, utilize -1 programmed ribosomal frameshifting (-1 PRF) for viral replication.
  • SARS-CoV-2 employs a distinctive RNA pseudoknotted structure to facilitate -1 PRF, presenting a potential therapeutic target.
  • Understanding the structural basis of SARS-CoV-2 -1 PRF pseudoknots is crucial for developing antiviral strategies.

Purpose of the Study:

  • To expand the knowledge of -1 PRF structural conformations across different coronaviruses.
  • To analyze and compare the -1 PRF pseudoknots of SARS-CoV-2, SARS-CoV, and MERS-CoV.
  • To investigate the impact of sequence mutations on the structure and function of these pseudoknots.

Main Methods:

  • Structural alignment approach to identify similarities in -1 PRF pseudoknots.
  • In-depth analysis of SARS-CoV-2 and MERS-CoV -1 PRF pseudoknots, including mutated sequences.
  • Introduction and application of Shapify, a novel algorithm integrating SHAPE data for RNA secondary structure prediction.

Main Results:

  • Identified similarities in -1 PRF pseudoknots among SARS-CoV-2, SARS-CoV, and MERS-CoV.
  • Provided detailed analysis of SARS-CoV-2 and MERS-CoV pseudoknot structures and the effects of mutations.
  • Shapify algorithm generated energetically favorable predictions, revealing novel folding pathways for the SARS-CoV-2 -1 PRF pseudoknot.

Conclusions:

  • The study enhances understanding of SARS-CoV-2 -1 PRF pseudoknot conformations and their structure-function relationships.
  • Predicted structures may correlate with -1 PRF efficiency, offering insights for therapeutic development.
  • Findings motivate further RNA structure-function research and aid in 3-D modeling of viral pseudoknots.